Mercurial > repos > matthias > dada2_plotqualityprofile

comparison dada2_plotQualityProfile.xml @ 5:863ebf0d28d5 draft

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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
author matthias
date Sun, 05 May 2019 12:26:15 -0400
parents cf166b8a8e27
children ec0479593908
comparison
equal deleted inserted replaced
4:4be2c17fd0b2 5:863ebf0d28d5
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="version_command"/> 7 <expand macro="version_command"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 Rscript --slave '$dada2_script' 9 ##name files by linking
10 #import re
11 #if "batch" in str($paired_cond.paired_select)
12 #set elid = re.sub('[^\w\-\.]', '_', str($paired_cond.fl.element_identifier))
13 #if "single" in str($paired_cond.paired_select)
14 ln -s '$paired_cond.fl' '$elid' &&
15 #else
16 ln -s '$paired_cond.fl.forward' '$elid'_forward &&
17 ln -s '$paired_cond.fl.reverse' '$elid'_reverse &&
18 #end if
19 #else
20 #for $read in $paired_cond.fl:
21 #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier))
22 #if "single" in str($paired_cond.paired_select)
23 ln -s '$read' '$elid' &&
24 #else
25 ln -s '$read.forward' '$elid'_forward &&
26 ln -s '$read.reverse' '$elid'_reverse &&
27 #end if
28 #end for
29 #end if
30
31 Rscript --slave '$dada2_script'
10 ]]></command> 32 ]]></command>
11 <configfiles> 33 <configfiles>
12 <configfile name="dada2_script"><![CDATA[ 34 <configfile name="dada2_script"><![CDATA[
35 #import re
13 files = c() 36 files = c()
14 #if "batch" in str($paired_cond.paired_select) 37 #if "batch" in str($paired_cond.paired_select)
38 #set elid = re.sub('[^\w\-\.]', '_', str($paired_cond.fl.element_identifier))
15 #if "single" in str($paired_cond.paired_select) 39 #if "single" in str($paired_cond.paired_select)
16 files = c(files, '$paired_cond.reads') 40 files = c(files, '$elid')
17 #else 41 #else
18 files = c(files, '$paired_cond.reads.forward') 42 files = c(files, paste('$elid', 'forward', sep = "_"))
19 files = c(files, '$paired_cond.reads.reverse') 43 files = c(files, paste('$elid', 'reverse', sep = "_"))
20 #end if 44 #end if
21 #else 45 #else
22 #for $read in $paired_cond.reads: 46 #for $read in $paired_cond.fl:
47 #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier))
23 #if "single" in str($paired_cond.paired_select) 48 #if "single" in str($paired_cond.paired_select)
24 files = c(files, '$read') 49 files = c(files, '$elid')
25 #else 50 #else
26 files = c(files, '$read.forward') 51 files = c(files, paste('$elid', 'forward', sep = "_"))
27 files = c(files, '$read.reverse') 52 files = c(files, paste('$elid', 'reverse', sep = "_"))
28 #end if 53 #end if
29 #end for 54 #end for
30 #end if 55 #end if
31 56
32 library(ggplot2, quietly=T) 57 library(ggplot2, quietly=T)
48 <option value="single">single - non batch</option> 73 <option value="single">single - non batch</option>
49 <option value="paired_batch">paired - batch</option> 74 <option value="paired_batch">paired - batch</option>
50 <option value="single_batch">single - batch</option> 75 <option value="single_batch">single - batch</option>
51 </param> 76 </param>
52 <when value="paired"> 77 <when value="paired">
53 <param name="reads" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz" label="Short read data"/> 78 <param argument="fl" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz" label="Short read data"/>
54 </when> 79 </when>
55 <when value="single"> 80 <when value="single">
56 <param name="reads" type="data" multiple="true" format="fastqsanger,fastqsanger.gz" label="Short read data"/> 81 <param argument="fl" type="data" multiple="true" format="fastqsanger,fastqsanger.gz" label="Short read data"/>
57 </when> 82 </when>
58 <when value="paired_batch"> 83 <when value="paired_batch">
59 <param name="reads" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz" label="Short read data"/> 84 <param argument="fl" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz" label="Short read data"/>
60 </when> 85 </when>
61 <when value="single_batch"> 86 <when value="single_batch">
62 <param name="reads" type="data" format="fastqsanger,fastqsanger.gz" label="Short read data"/> 87 <param argument="fl" type="data" format="fastqsanger,fastqsanger.gz" label="Short read data"/>
63 </when> 88 </when>
64 </conditional> 89 </conditional>
65 <param argument="aggregate" type="boolean" label="Aggregate data" checked="True" truevalue="TRUE" falsevalue="FALSE" help="Create a single plot for all data sets (default) or a separate plot for each data set"/> 90 <param argument="aggregate" type="boolean" label="Aggregate data" checked="True" truevalue="TRUE" falsevalue="FALSE" help="Create a single plot for all data sets (default) or a separate plot for each data set"/>
66 <param argument="n" type="integer" value="500000" label="sample number" help="number of records to sample from the fastq file"/> 91 <param argument="n" type="integer" value="500000" label="sample number" help="number of records to sample from the fastq file"/>
67 </inputs> 92 </inputs>
71 <tests> 96 <tests>
72 <!-- paired non-batch, aggregate --> 97 <!-- paired non-batch, aggregate -->
73 <test> 98 <test>
74 <param name="aggregate" value="TRUE"/> 99 <param name="aggregate" value="TRUE"/>
75 <param name="paired_cond|paired_select" value="paired"/> 100 <param name="paired_cond|paired_select" value="paired"/>
76 <param name="paired_cond|reads"> 101 <param name="paired_cond|fl">
77 <collection type="list:paired"> 102 <collection type="list:paired">
78 <element name="F3D0_S188_L001"> 103 <element name="F3D0_S188_L001">
79 <collection type="paired"> 104 <collection type="paired">
80 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> 105 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
81 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> 106 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
87 </test> 112 </test>
88 <!-- paired, batch, no aggregate--> 113 <!-- paired, batch, no aggregate-->
89 <test> 114 <test>
90 <param name="aggregate" value="FALSE"/> 115 <param name="aggregate" value="FALSE"/>
91 <param name="paired_cond|paired_select" value="paired_batch"/> 116 <param name="paired_cond|paired_select" value="paired_batch"/>
92 <param name="paired_cond|reads"> 117 <param name="paired_cond|fl">
93 <collection type="paired"> 118 <collection type="paired">
94 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> 119 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
95 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> 120 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
96 </collection> 121 </collection>
97 </param> 122 </param>
99 </test> 124 </test>
100 <!-- single, non-batch, aggregate --> 125 <!-- single, non-batch, aggregate -->
101 <test> 126 <test>
102 <param name="aggregate" value="TRUE"/> 127 <param name="aggregate" value="TRUE"/>
103 <param name="paired_cond|paired_select" value="single"/> 128 <param name="paired_cond|paired_select" value="single"/>
104 <param name="paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz,F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> 129 <param name="paired_cond|fl" value="F3D0_S188_L001_R1_001.fastq.gz,F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
105 <param name="n" value="10000"/> 130 <param name="n" value="10000"/>
106 <output name="output" value="qualityProfileSmallSample.pdf" ftype="pdf"/> 131 <output name="output" value="qualityProfileSmallSample.pdf" ftype="pdf"/>
107 </test> 132 </test>
108 <!-- single, batch, no aggregate --> 133 <!-- single, batch, no aggregate -->
109 <test> 134 <test>
110 <param name="aggregate" value="FALSE"/> 135 <param name="aggregate" value="FALSE"/>
111 <param name="paired_cond|paired_select" value="single_batch"/> 136 <param name="paired_cond|paired_select" value="single_batch"/>
112 <param name="paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> 137 <param name="paired_cond|fl" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
113 <param name="n" value="10000"/> 138 <param name="n" value="10000"/>
114 <output name="output" value="qualityProfileSmallSample.pdf" ftype="pdf" compare="sim_size"/> 139 <output name="output" value="qualityProfileSmallSample.pdf" ftype="pdf" compare="sim_size"/>
115 </test> </tests> 140 </test> </tests>
116 <help><![CDATA[ 141 <help><![CDATA[
117 Summary 142 Summary